molt_dat <- read.csv("../data/wl_molt_dat.csv")
# read in .csv

library(dplyr)
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
library(car)
## Loading required package: carData
## 
## Attaching package: 'car'
## The following object is masked from 'package:dplyr':
## 
##     recode
library(ggplot2)
# load relevant libraries for stats analysis
plot(hemo_ri ~ days_from_molt, data = molt_dat,
     main = "Hemolymph RI as Green Crabs Approach Molt (n=13)",
     xlim = rev(range(days_from_molt)),
     xlab = "Days From Molt", 
     ylab = "Hemolymph RI",
     type = "b")
abline(lm (hemo_ri ~ days_from_molt, data = molt_dat), col = 4, lwd = 3)

# plots hemo ri vs days from molt for all 13 crabs
# need to reverse x axis to count down to molt
# appears to be downward trend in hemolymph RI as crabs approach molt
# need to investigate on an individual level
molt_dat %>% 
        # pipes molt data into ggplot
  ggplot(aes(x = days_from_molt, y = hemo_ri)) + 
        # populates plot with hemo ri info and defines color with crab ID
    geom_point() + geom_smooth(method=lm) + 
        # specifies type of plot -- linear model with 95 percent confidence
        scale_x_reverse() + 
        # reverses x axis so information counts down to molt
        xlab("Days from molt") + 
        ylab ("Hemolymph RI") +
        ggtitle("Hemolymph RI as green crabs approach molt (n = 13)")
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 5 rows containing non-finite values (stat_smooth).
## Warning: Removed 5 rows containing missing values (geom_point).

        # renames x and y labels and title
molt_dat %>% 
        # pipes molt data into ggplot
  ggplot(aes(x = days_from_molt, y = hemo_ri)) + 
        # populates plot with hemo ri info and defines color with crab ID
    geom_point() + geom_smooth(method=lm, se=FALSE) + 
        # specifies type of plot -- linear model without confidence int
        scale_x_reverse() + 
        # reverses x axis so information counts down to molt
        xlab("Days from molt") + 
        ylab ("Hemolymph RI") +
        ggtitle("Hemolymph RI as green crabs approach molt (n = 13)")
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 5 rows containing non-finite values (stat_smooth).
## Warning: Removed 5 rows containing missing values (geom_point).

        # renames x and y labels and title
library(ggplot2)
library(dplyr)

molt_dat %>% 
        # pipes molt data into ggplot
  ggplot(aes(x = days_from_molt, y = hemo_ri, colour = crab_id)) + 
        # populates plot with hemo ri info and defines color with crab ID
    geom_point() + geom_line() + 
        # specifies type of plot - scatter linear plot with crab IDs
        scale_x_reverse() + 
        # reverses x axis so information counts down to molt
        xlab("Days from molt") + 
        ylab ("Hemolymph RI") +
        ggtitle("Hemolymph RI as green crabs approach molt (n = 13)") +
        # renames x and y labels and title
        labs(col = "Crab ID") 
## Warning: Removed 5 rows containing missing values (geom_point).
## Warning: Removed 5 row(s) containing missing values (geom_path).

        # changes legend title
library(ggplot2)
library(dplyr)

molt_dat %>% 
        # pipes molt data into ggplot
  ggplot(aes(x = days_from_molt, y = hemo_ri, colour = crab_id)) + 
        # populates plot with hemo ri info and defines color with crab ID
    geom_point() + geom_line() +
        # specifies type of plot - scatter linear plot with crab ids
        scale_x_reverse() + 
        # reverses x axis so information counts down to molt
        xlab("Days from molt") + 
        ylab ("Hemolymph RI") +
        ggtitle("Hemolymph RI as green crabs approach molt (n = 13)") +
        # renames x and y labels and title
        labs(col = "Crab ID") + 
        # changes legend title
        theme(panel.grid.major = element_blank(),
              panel.grid.minor = element_blank(), 
              panel.background = element_blank())
## Warning: Removed 5 rows containing missing values (geom_point).
## Warning: Removed 5 row(s) containing missing values (geom_path).

        # removes background grid from plot
ri_mod <- lm(hemo_ri ~ days_from_molt, data = molt_dat)
summary(ri_mod)
## 
## Call:
## lm(formula = hemo_ri ~ days_from_molt, data = molt_dat)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -4.3899 -1.7526 -0.1578  1.9173  4.3814 
## 
## Coefficients:
##                Estimate Std. Error t value Pr(>|t|)    
## (Intercept)     5.75255    0.49221  11.687  < 2e-16 ***
## days_from_molt  0.17321    0.04246   4.079 0.000137 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 2.238 on 59 degrees of freedom
##   (5 observations deleted due to missingness)
## Multiple R-squared:   0.22,  Adjusted R-squared:  0.2068 
## F-statistic: 16.64 on 1 and 59 DF,  p-value: 0.0001374
anova(ri_mod)
## Analysis of Variance Table
## 
## Response: hemo_ri
##                Df Sum Sq Mean Sq F value    Pr(>F)    
## days_from_molt  1  83.31  83.310   16.64 0.0001374 ***
## Residuals      59 295.39   5.007                      
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
car::Anova(ri_mod, type = 3)
## Anova Table (Type III tests)
## 
## Response: hemo_ri
##                Sum Sq Df F value    Pr(>F)    
## (Intercept)    683.85  1  136.59 < 2.2e-16 ***
## days_from_molt  83.31  1   16.64 0.0001374 ***
## Residuals      295.39 59                      
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
# linear models for significance testing 
# r square of 0.22 -- weak correlation
plot(hemo_color ~ days_from_molt, data = molt_dat,
     main = "Hemolymph Color as Green Crabs Approach Molt (n=13)",
     xlim = rev(range(days_from_molt)),
     xlab = "Days From Molt", 
     ylab = "Hemolymph Color")
abline(lm (hemo_color ~ days_from_molt, data = molt_dat), col = 4, lwd = 3)

boxplot(days_from_molt ~ hemo_color, data = molt_dat)

# plots hemo color vs days from molt for all 13 crabs
# need to reverse x axis to count down to molt
# doesn't appear to be strong trend or correlation
library(ggplot2)
library(dplyr)

molt_dat %>% 
        # pipes molt data into ggplot
  ggplot(aes(x = days_from_molt, y = hemo_color, colour = crab_id)) + 
        # populates plot with hemo color info and defines color with crab ID
    geom_point() + geom_line() + 
        # specifies type of plot
        scale_x_reverse() + 
        # reverses x axis so information counts down to molt
        xlab("Days from molt") + 
        ylab ("Hemolymph Color") +
        ggtitle("Hemolymph color as green crabs approach molt (n = 13") +
        # renames x and y labels and title
        labs(col = "Crab ID")
## Warning: Removed 5 rows containing missing values (geom_point).
## Warning: Removed 5 row(s) containing missing values (geom_path).

        # changes legend title
col_mod <- lm(hemo_color ~ days_from_molt, data = molt_dat)
summary(col_mod)
## 
## Call:
## lm(formula = hemo_color ~ days_from_molt, data = molt_dat)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -1.96848  0.03152  0.16184  0.22198  2.16184 
## 
## Coefficients:
##                Estimate Std. Error t value Pr(>|t|)    
## (Intercept)     2.75797    0.19716  13.989   <2e-16 ***
## days_from_molt  0.01002    0.01701   0.589    0.558    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.8963 on 59 degrees of freedom
##   (5 observations deleted due to missingness)
## Multiple R-squared:  0.005853,   Adjusted R-squared:  -0.011 
## F-statistic: 0.3474 on 1 and 59 DF,  p-value: 0.5579
anova(col_mod)
## Analysis of Variance Table
## 
## Response: hemo_color
##                Df Sum Sq Mean Sq F value Pr(>F)
## days_from_molt  1  0.279 0.27903  0.3474 0.5579
## Residuals      59 47.393 0.80327
car::Anova(col_mod, type = 3)
## Anova Table (Type III tests)
## 
## Response: hemo_color
##                 Sum Sq Df  F value Pr(>F)    
## (Intercept)    157.187  1 195.6833 <2e-16 ***
## days_from_molt   0.279  1   0.3474 0.5579    
## Residuals       47.393 59                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
# linear models for significance testing 
# individual hemo color graphs over time

plot(hemo_color ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GBGB",
     xlab = "Days From Molt", 
     ylab = "Hemolymph Color",
     type = "b")

plot(hemo_color ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GBGG",
     xlab = "Days From Molt", 
     ylab = "Hemolymph Color",
     type = "b")

plot(hemo_color ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GBGB",
     xlab = "Days From Molt", 
     ylab = "Hemolymph Color",
     type = "b")

plot(hemo_color ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GBGY",
     xlab = "Days From Molt", 
     ylab = "Hemolymph Color",
     type = "b")

plot(hemo_color ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GBKR",
     xlab = "Days From Molt", 
     ylab = "Hemolymph Color",
     type = "b")

plot(hemo_color ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GBWK",
     xlab = "Days From Molt", 
     ylab = "Hemolymph Color",
     type = "b")

plot(hemo_color ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GBYB",
     xlab = "Days From Molt", 
     ylab = "Hemolymph Color",
     type = "b")

plot(hemo_color ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GGBR",
     xlab = "Days From Molt", 
     ylab = "Hemolymph Color",
     type = "b")

plot(hemo_color ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GGBY",
     xlab = "Days From Molt", 
     ylab = "Hemolymph Color",
     type = "b")

plot(hemo_color ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GGGW",
     xlab = "Days From Molt", 
     ylab = "Hemolymph Color",
     type = "b")

plot(hemo_color ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GGGY",
     xlab = "Days From Molt", 
     ylab = "Hemolymph Color",
     type = "b")

plot(hemo_color ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GGKG",
     xlab = "Days From Molt", 
     ylab = "Hemolymph Color",
     type = "b")

plot(hemo_color ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GGKR",
     xlab = "Days From Molt", 
     ylab = "Hemolymph Color",
     type = "b")

plot(hemo_color ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GGW",
     xlab = "Days From Molt", 
     ylab = "Hemolymph Color",
     type = "b")

# individual RI graphs over time
# appears that as crabs approach molt, RI decreases

plot(hemo_ri ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GBGB",
     xlab = "Days From Molt",
     type = "b")

plot(hemo_ri ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GBGG",
     xlab = "Days From Molt", 
     ylab = "Hemolymph RI",
     type = "b")

plot(hemo_ri ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GBGB",
     xlab = "Days From Molt", 
     ylab = "Hemolymph RI",
     type = "b")

plot(hemo_ri ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GBGY",
     xlab = "Days From Molt", 
     ylab = "Hemolymph RI",
     type = "b")

plot(hemo_ri ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GBKR",
     xlab = "Days From Molt", 
     ylab = "Hemolymph RI",
     type = "b")

plot(hemo_ri ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GBWK",
     xlab = "Days From Molt", 
     ylab = "Hemolymph RI",
     type = "b")

plot(hemo_ri ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GBYB",
     xlab = "Days From Molt", 
     ylab = "Hemolymph RI",
     type = "b")

plot(hemo_ri ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GGBR",
     xlab = "Days From Molt", 
     ylab = "Hemolymph RI",
     type = "b")

plot(hemo_ri ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GGBY",
     xlab = "Days From Molt", 
     ylab = "Hemolymph RI",
     type = "b")

plot(hemo_ri ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GGGW",
     xlab = "Days From Molt", 
     ylab = "Hemolymph RI",
     type = "b")

plot(hemo_ri ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GGGY",
     xlab = "Days From Molt", 
     ylab = "Hemolymph RI",
     type = "b")

plot(hemo_ri ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GGKG",
     xlab = "Days From Molt", 
     ylab = "Hemolymph RI",
     type = "b")

plot(hemo_ri ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GGKR",
     xlab = "Days From Molt", 
     ylab = "Hemolymph RI",
     type = "b")

plot(hemo_ri ~ days_from_molt, data = molt_dat,
     subset = crab_id == "GGW",
     xlab = "Days From Molt", 
     ylab = "Hemolymph RI",
     type = "b")